1
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Huang L, Chen X, Yang X, Zhang Y, Liang Y, Qiu X. Elucidating epigenetic mechanisms governing odontogenic differentiation in dental pulp stem cells: an in-depth exploration. Front Cell Dev Biol 2024; 12:1394582. [PMID: 38863943 PMCID: PMC11165363 DOI: 10.3389/fcell.2024.1394582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024] Open
Abstract
Epigenetics refers to the mechanisms such as DNA methylation and histone modification that influence gene expression without altering the DNA sequence. These epigenetic modifications can regulate gene transcription, splicing, and stability, thereby impacting cell differentiation, development, and disease occurrence. The formation of dentin is intrinsically linked to the odontogenic differentiation of dental pulp stem cells (DPSCs), which are recognized as the optimal cell source for dentin-pulp regeneration due to their varied odontogenic potential, strong proliferative and angiogenic characteristics, and ready accessibility Numerous studies have demonstrated the critical role of epigenetic regulation in DPSCs differentiation into specific cell types. This review thus provides a comprehensive review of the mechanisms by which epigenetic regulation controls the odontogenesis fate of DPSCs.
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Affiliation(s)
| | | | | | | | | | - Xiaoling Qiu
- Department of Endodontics, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
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2
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Jin SW, Seong Y, Yoon D, Kwon YS, Song H. Dissolution of ribonucleoprotein condensates by the embryonic stem cell protein L1TD1. Nucleic Acids Res 2024; 52:3310-3326. [PMID: 38165001 PMCID: PMC11014241 DOI: 10.1093/nar/gkad1244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 11/22/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024] Open
Abstract
L1TD1 is a cytoplasmic RNA-binding protein specifically expressed in pluripotent stem cells and, unlike its mouse ortholog, is essential for the maintenance of stemness in human cells. Although L1TD1 is the only known protein-coding gene domesticated from a LINE-1 (L1) retroelement, the functional legacy of its ancestral protein, ORF1p of L1, and how it is manifested in L1TD1 are still unknown. Here, we determined RNAs associated with L1TD1 and found that, like ORF1p, L1TD1 binds L1 RNAs and localizes to high-density ribonucleoprotein (RNP) condensates. Unexpectedly, L1TD1 enhanced the translation of a subset of mRNAs enriched in the condensates. L1TD1 depletion promoted the formation of stress granules in embryonic stem cells. In HeLa cells, ectopically expressed L1TD1 facilitated the dissolution of stress granules and granules formed by pathological mutations of TDP-43 and FUS. The glutamate-rich domain and the ORF1-homology domain of L1TD1 facilitated dispersal of the RNPs and induced autophagy, respectively. These results provide insights into how L1TD1 regulates gene expression in pluripotent stem cells. We propose that the ability of L1TD1 to dissolve stress granules may provide novel opportunities for treatment of neurodegenerative diseases caused by disturbed stress granule dynamics.
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Affiliation(s)
- Sang Woo Jin
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Youngmo Seong
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Dayoung Yoon
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Young-Soo Kwon
- Department of Integrative Bioscience & Biotechnology, Sejong University, Seoul 05006, Republic of Korea
| | - Hoseok Song
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
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3
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Kwon YS, Jin SW, Song H. Global analysis of binding sites of U2AF1 and ZRSR2 reveals RNA elements required for mutually exclusive splicing by the U2- and U12-type spliceosome. Nucleic Acids Res 2024; 52:1420-1434. [PMID: 38088204 PMCID: PMC10853781 DOI: 10.1093/nar/gkad1180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 11/18/2023] [Accepted: 12/05/2023] [Indexed: 02/10/2024] Open
Abstract
Recurring mutations in genes encoding 3' splice-site recognition proteins, U2AF1 and ZRSR2 are associated with human cancers. Here, we determined binding sites of the proteins to reveal that U2-type and U12-type splice sites are recognized by U2AF1 and ZRSR2, respectively. However, some sites are spliced by both the U2-type and U12-type spliceosomes, indicating that well-conserved consensus motifs in some U12-type introns could be recognized by the U2-type spliceosome. Nucleotides flanking splice sites of U12-type introns are different from those flanking U2-type introns. Remarkably, the AG dinucleotide at the positions -1 and -2 of 5' splice sites of U12-type introns with GT-AG termini is not present. AG next to 5' splice site introduced by a single nucleotide substitution at the -2 position could convert a U12-type splice site to a U2-type site. The class switch of introns by a single mutation and the bias against G at the -1 position of U12-type 5' splice site support the notion that the identities of nucleotides in exonic regions adjacent to splice sites are fine-tuned to avoid recognition by the U2-type spliceosome. These findings may shed light on the mechanism of selectivity in U12-type intron splicing and the mutations that affect splicing.
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Affiliation(s)
- Young-Soo Kwon
- Department of Integrative Bioscience & Biotechnology, Sejong University, Seoul 05006, Korea
| | - Sang Woo Jin
- BK21 Graduate Program, Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul 08308, Korea
| | - Hoseok Song
- BK21 Graduate Program, Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul 08308, Korea
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4
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Nguyen TL, Nguyen TD, Ngo MK, Le TNY, Nguyen TA. Noncanonical processing by animal Microprocessor. Mol Cell 2023; 83:1810-1826.e8. [PMID: 37267903 DOI: 10.1016/j.molcel.2023.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 04/06/2023] [Accepted: 05/03/2023] [Indexed: 06/04/2023]
Abstract
Microprocessor (MP), DROSHA-DGCR8, processes primary miRNA transcripts (pri-miRNAs) to initiate miRNA biogenesis. The canonical cleavage mechanism of MP has been extensively investigated and comprehensively validated for two decades. However, this canonical mechanism cannot account for the processing of certain pri-miRNAs in animals. In this study, by conducting high-throughput pri-miRNA cleavage assays for approximately 260,000 pri-miRNA sequences, we discovered and comprehensively characterized a noncanonical cleavage mechanism of MP. This noncanonical mechanism does not need several RNA and protein elements essential for the canonical mechanism; instead, it utilizes previously unrecognized DROSHA dsRNA recognition sites (DRESs). Interestingly, the noncanonical mechanism is conserved across animals and plays a particularly significant role in C. elegans. Our established noncanonical mechanism elucidates MP cleavage in numerous RNA substrates unaccounted for by the canonical mechanism in animals. This study suggests a broader substrate repertoire of animal MPs and an expanded regulatory landscape for miRNA biogenesis.
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Affiliation(s)
- Thuy Linh Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Trung Duc Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Minh Khoa Ngo
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Thi Nhu-Y Le
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Tuan Anh Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China.
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5
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Liu Y, Gan L, Cui DX, Yu SH, Pan Y, Zheng LW, Wan M. Epigenetic regulation of dental pulp stem cells and its potential in regenerative endodontics. World J Stem Cells 2021; 13:1647-1666. [PMID: 34909116 PMCID: PMC8641018 DOI: 10.4252/wjsc.v13.i11.1647] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/07/2021] [Accepted: 11/03/2021] [Indexed: 02/06/2023] Open
Abstract
Regenerative endodontics (RE) therapy means physiologically replacing damaged pulp tissue and regaining functional dentin–pulp complex. Current clinical RE procedures recruit endogenous stem cells from the apical papilla, periodontal tissue, bone marrow and peripheral blood, with or without application of scaffolds and growth factors in the root canal space, resulting in cementum-like and bone-like tissue formation. Without the involvement of dental pulp stem cells (DPSCs), it is unlikely that functional pulp regeneration can be achieved, even though acceptable repair can be acquired. DPSCs, due to their specific odontogenic potential, high proliferation, neurovascular property, and easy accessibility, are considered as the most eligible cell source for dentin–pulp regeneration. The regenerative potential of DPSCs has been demonstrated by recent clinical progress. DPSC transplantation following pulpectomy has successfully reconstructed neurovascularized pulp that simulates the physiological structure of natural pulp. The self-renewal, proliferation, and odontogenic differentiation of DPSCs are under the control of a cascade of transcription factors. Over recent decades, epigenetic modulations implicating histone modifications, DNA methylation, and noncoding (nc)RNAs have manifested as a new layer of gene regulation. These modulations exhibit a profound effect on the cellular activities of DPSCs. In this review, we offer an overview about epigenetic regulation of the fate of DPSCs; in particular, on the proliferation, odontogenic differentiation, angiogenesis, and neurogenesis. We emphasize recent discoveries of epigenetic molecules that can alter DPSC status and promote pulp regeneration through manipulation over epigenetic profiles.
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Affiliation(s)
- Ying Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Lu Gan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Di-Xin Cui
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Si-Han Yu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Yue Pan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Li-Wei Zheng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Mian Wan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
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6
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XPO5 promotes primary miRNA processing independently of RanGTP. Nat Commun 2020; 11:1845. [PMID: 32296071 PMCID: PMC7160132 DOI: 10.1038/s41467-020-15598-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 03/17/2020] [Indexed: 12/24/2022] Open
Abstract
XPO5 mediates nuclear export of miRNA precursors in a RanGTP-dependent manner. However, XPO5-associated RNA species have not been determined globally and it is unclear whether XPO5 has any additional functions other than nuclear export. Here we show XPO5 pervasively binds to double-stranded RNA regions found in some clustered primary miRNA precursors and many cellular RNAs. Surprisingly, the binding of XPO5 to pri-miRNAs such as mir-17~92 and mir-15b~16-2 and highly structured RNAs such as vault RNAs is RanGTP-independent. Importantly, XPO5 enhances the processing efficiency of pri-mir-19a and mir-15b~16-2 by the DROSHA/DGCR8 microprocessor. Genetic deletion of XPO5 compromises the biogenesis of most miRNAs and leads to severe defects during mouse embryonic development and skin morphogenesis. This study reveals an unexpected function of XPO5 for recognizing and facilitating the nuclear cleavage of clustered pri-miRNAs, identifies numerous cellular RNAs bound by XPO5, and demonstrates physiological functions of XPO5 in mouse development. XPO5 mediates nuclear export of miRNA hairpin precursors (pre-miRNAs) through a RanGTP-dependent binding. Here the authors employ HITS-CLIP and biochemical analysis and show that XPO5 binds and promotes nuclear processing of clustered pri-miRNAs, with extensive double-stranded regions, independently of RanGTP.
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7
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Nguyen TL, Nguyen TD, Bao S, Li S, Nguyen TA. The internal loops in the lower stem of primary microRNA transcripts facilitate single cleavage of human Microprocessor. Nucleic Acids Res 2020; 48:2579-2593. [PMID: 31956890 PMCID: PMC7049713 DOI: 10.1093/nar/gkaa018] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 01/02/2020] [Accepted: 01/06/2020] [Indexed: 12/23/2022] Open
Abstract
The human Microprocessor complex cleaves primary microRNA (miRNA) transcripts (pri-miRNAs) to initiate miRNA synthesis. Microprocessor consists of DROSHA (an RNase III enzyme), and DGCR8. DROSHA contains two RNase III domains, RIIIDa and RIIIDb, which simultaneously cleave the 3p- and 5p-strands of pri-miRNAs, respectively. In this study, we show that the internal loop located in the lower stem of numerous pri-miRNAs selectively inhibits the cleavage of Microprocessor on their 3p-strand, thereby, facilitating the single cleavage on their 5p-strand. This single cleavage does not lead to the production of miRNA but instead, it downregulates miRNA expression. We also demonstrate that by manipulating the size of the internal loop in the lower stem of pri-miRNAs, we can alter the ratio of single-cut to double-cut products resulted from the catalysis of Microprocessor, thus changing miRNA production in the in vitro pri-miRNA processing assays and in human cells. Therefore, the oscillating level of the single cleavage suggests another way of regulation of miRNA expression and offers an alternative approach to miRNA knockdown.
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Affiliation(s)
- Thuy Linh Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Trung Duc Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Sheng Bao
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Shaohua Li
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Tuan Anh Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
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8
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Sabry R, Yamate J, Favetta L, LaMarre J. MicroRNAs: potential targets and agents of endocrine disruption in female reproduction. J Toxicol Pathol 2019; 32:213-221. [PMID: 31719748 PMCID: PMC6831493 DOI: 10.1293/tox.2019-0054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs are short non-coding RNAs that have been widely recognized as key mediators in the epigenetic control of gene expression and which are present in virtually all cells and tissues studied. These regulatory molecules are generated in multiple steps in a process called microRNA biogenesis. Distinct microRNA expression patterns during the different stages of oocyte and embryo development suggest important regulatory roles for these small RNAs. Moreover, studies antagonizing specific microRNAs and enzymes in microRNA biogenesis pathways have demonstrated that interference with normal miRNA function leads to infertility and is associated with some reproductive abnormalities. Endocrine disrupting chemicals such as Bisphenol A (BPA) are synthetic hormone mimics that have been found to negatively impact reproductive health. In addition to their direct effects on gene expression, these chemicals are widely implicated in the disruption of epigenetic pathways, including the expression and activity of miRNAs, thereby altering gene expression. In this review, the roles of microRNAs during mammalian oocyte and embryo development are outlined and the different mechanisms by which endocrine disruptors such as BPA interfere with these epigenetic regulators to cause reproductive problems is explored.
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Affiliation(s)
- Reem Sabry
- Reproductive Health and Biotechnology Laboratory, Biomedical Sciences, Ontario Veterinary College, University of Guelph, 28 College Ave W, Guelph, ON, N1G 2W1, Canada
| | - Jyoji Yamate
- Laboratory of Veterinary Pathology, Osaka Prefecture University, 1-58 Rinku-Ourai Kita, Izumisano, Osaka 598-8531, Japan
| | - Laura Favetta
- Reproductive Health and Biotechnology Laboratory, Biomedical Sciences, Ontario Veterinary College, University of Guelph, 28 College Ave W, Guelph, ON, N1G 2W1, Canada
| | - Jonathan LaMarre
- Reproductive Health and Biotechnology Laboratory, Biomedical Sciences, Ontario Veterinary College, University of Guelph, 28 College Ave W, Guelph, ON, N1G 2W1, Canada
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9
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Zhang J, Bai R, Li M, Ye H, Wu C, Wang C, Li S, Tan L, Mai D, Li G, Pan L, Zheng Y, Su J, Ye Y, Fu Z, Zheng S, Zuo Z, Liu Z, Zhao Q, Che X, Xie D, Jia W, Zeng MS, Tan W, Chen R, Xu RH, Zheng J, Lin D. Excessive miR-25-3p maturation via N 6-methyladenosine stimulated by cigarette smoke promotes pancreatic cancer progression. Nat Commun 2019; 10:1858. [PMID: 31015415 PMCID: PMC6478927 DOI: 10.1038/s41467-019-09712-x] [Citation(s) in RCA: 241] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/26/2019] [Indexed: 12/15/2022] Open
Abstract
N6-methyladenosine (m6A) modification is an important mechanism in miRNA processing and maturation, but the role of its aberrant regulation in human diseases remained unclear. Here, we demonstrate that oncogenic primary microRNA-25 (miR-25) in pancreatic duct epithelial cells can be excessively maturated by cigarette smoke condensate (CSC) via enhanced m6A modification that is mediated by NF-κB associated protein (NKAP). This modification is catalyzed by overexpressed methyltransferase-like 3 (METTL3) due to hypomethylation of the METTL3 promoter also caused by CSC. Mature miR-25, miR-25-3p, suppresses PH domain leucine-rich repeat protein phosphatase 2 (PHLPP2), resulting in the activation of oncogenic AKT-p70S6K signaling, which provokes malignant phenotypes of pancreatic cancer cells. High levels of miR-25-3p are detected in smokers and in pancreatic cancers tissues that are correlated with poor prognosis of pancreatic cancer patients. These results collectively indicate that cigarette smoke-induced miR-25-3p excessive maturation via m6A modification promotes the development and progression of pancreatic cancer.
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MESH Headings
- Adenosine/analogs & derivatives
- Adenosine/metabolism
- Adult
- Aged
- Aged, 80 and over
- Carcinoma, Pancreatic Ductal/blood
- Carcinoma, Pancreatic Ductal/etiology
- Carcinoma, Pancreatic Ductal/mortality
- Carcinoma, Pancreatic Ductal/pathology
- Cell Line, Tumor
- Cell Transformation, Neoplastic/genetics
- Co-Repressor Proteins/metabolism
- DNA Methylation
- Disease Progression
- Epithelial Cells/pathology
- Female
- Follow-Up Studies
- Gene Expression Regulation, Neoplastic
- HEK293 Cells
- Humans
- Male
- Methyltransferases/genetics
- Methyltransferases/metabolism
- MicroRNAs/blood
- MicroRNAs/metabolism
- Middle Aged
- Nuclear Proteins/metabolism
- Pancreatic Ducts/cytology
- Pancreatic Ducts/pathology
- Pancreatic Neoplasms/blood
- Pancreatic Neoplasms/etiology
- Pancreatic Neoplasms/mortality
- Pancreatic Neoplasms/pathology
- Phosphoprotein Phosphatases/genetics
- Phosphoprotein Phosphatases/metabolism
- Prognosis
- Promoter Regions, Genetic/genetics
- Proto-Oncogene Proteins c-akt/metabolism
- RNA-Binding Proteins/metabolism
- Repressor Proteins
- Ribosomal Protein S6 Kinases, 70-kDa/metabolism
- Smoke/adverse effects
- Smoking/adverse effects
- Smoking/blood
- Nicotiana/toxicity
- Up-Regulation
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Affiliation(s)
- Jialiang Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Ruihong Bai
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Mei Li
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Huilin Ye
- Department of Pancreaticobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chen Wu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- CAMS Key Laboratory of Genetics and Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chengfeng Wang
- Department of Abdominal Surgery, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shengping Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Liping Tan
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Dongmei Mai
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Guolin Li
- Department of Pancreaticobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ling Pan
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yanfen Zheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jiachun Su
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Ying Ye
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zhiqiang Fu
- Department of Pancreaticobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shangyou Zheng
- Department of Pancreaticobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhixiang Zuo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zexian Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Qi Zhao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xu Che
- Department of Abdominal Surgery, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dan Xie
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Weihua Jia
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Mu-Sheng Zeng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Wen Tan
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- CAMS Key Laboratory of Genetics and Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rufu Chen
- Department of Pancreaticobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Rui-Hua Xu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
| | - Jian Zheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
| | - Dongxin Lin
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- CAMS Key Laboratory of Genetics and Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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10
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Jung E, Seong Y, Jeon B, Kwon YS, Song H. MicroRNAs of miR-17-92 cluster increase gene expression by targeting mRNA-destabilization pathways. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:603-612. [PMID: 29935344 DOI: 10.1016/j.bbagrm.2018.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/27/2018] [Accepted: 06/15/2018] [Indexed: 01/07/2023]
Abstract
MicroRNAs (miRNAs) of the miR-17-92 cluster are overexpressed in human cancers, and their enforced expression is tumorigenic in mouse models. A number of genes are reported to be targets of these miRNAs and are implicated in their tumorigenic potential. However, the mode of action by miRNAs suggests that global analysis of their targets is required to understand their cellular roles. In this study, we globally analyzed AGO2-bound mRNAs and found that the miR-17-92 miRNAs coherently repress multiple targets involved in the destabilization of mRNA. While the miRNAs repress the expression of their targets, they increase stability and lengthen the poly-A tails of non-target mRNAs. Furthermore, the expression of BTG3, TOB1, CSNK1A1 and ANKRD52 is negatively correlated with the expression of the miR-17-92 cluster in cancer cell lines. Our results suggest that the miR-17-92 miRNAs promote tumorigenesis not only by repression of key regulators, but also by posttranscriptional increases of global gene expression.
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Affiliation(s)
- Eunsun Jung
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Youngmo Seong
- Department of Bioscience & Biotechnology, Sejong University, Seoul 05006, Republic of Korea
| | - Bohyun Jeon
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Young-Soo Kwon
- Department of Bioscience & Biotechnology, Sejong University, Seoul 05006, Republic of Korea.
| | - Hoseok Song
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea.
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11
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Creugny A, Fender A, Pfeffer S. Regulation of primary microRNA processing. FEBS Lett 2018; 592:1980-1996. [PMID: 29683487 DOI: 10.1002/1873-3468.13067] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 12/28/2022]
Abstract
MicroRNAs (miRNAs) are evolutionarily conserved small regulatory RNAs that participate in the adjustment of many, if not all, fundamental biological processes. Molecular mechanisms involved in miRNA biogenesis and mode of action have been elucidated in the past two decades. Similar to many cellular pathways, miRNA processing and function can be globally or specifically regulated at several levels and by numerous proteins and RNAs. Given their role as fine-tuning molecules, it is essential for miRNA expression to be tightly regulated in order to maintain cellular homeostasis. Here, we review our current knowledge of the first step of their maturation occurring in the nucleus and how it can be specifically and dynamically modulated.
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Affiliation(s)
- Antoine Creugny
- Architecture and Reactivity of RNA, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, France
| | - Aurélie Fender
- Architecture and Reactivity of RNA, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, France
| | - Sébastien Pfeffer
- Architecture and Reactivity of RNA, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, France
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12
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Lim DH, Lee S, Han JY, Choi MS, Hong JS, Seong Y, Kwon YS, Lee YS. Ecdysone-responsive microRNA-252-5p controls the cell cycle by targeting Abi in Drosophila. FASEB J 2018. [PMID: 29543534 DOI: 10.1096/fj.201701185rr] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The steroid hormone ecdysone has a central role in the developmental transitions of insects through its control of responsive protein-coding and microRNA (miRNA) gene expression. However, the complete regulatory network controlling the expression of these genes remains to be elucidated. In this study, we performed cross-linking immunoprecipitation coupled with deep sequencing of endogenous Argonaute 1 (Ago1) protein, the core effector of the miRNA pathway, in Drosophila S2 cells. We found that regulatory interactions between miRNAs and their cognate targets were substantially altered by Ago1 in response to ecdysone signaling. Additionally, during the larva-to-adult metamorphosis, miR-252-5p was up-regulated via the canonical ecdysone-signaling pathway. Moreover, we provide evidence that miR-252-5p targets Abelson interacting protein ( Abi) to decrease the protein levels of cyclins A and B, controlling the cell cycle. Overall, our data suggest a potential role for the ecdysone/miR-252-5p/Abi regulatory axis partly in cell-cycle control during metamorphosis in Drosophila.-Lim, D.-H., Lee, S., Han, J. Y., Choi, M.-S., Hong, J.-S., Seong, Y., Kwon, Y.-S., Lee, Y. S. Ecdysone-responsive microR-252-5p controls the cell cycle by targeting Abi in Drosophila.
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Affiliation(s)
- Do-Hwan Lim
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, South Korea
| | - Seungjae Lee
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, South Korea
| | - Jee Yun Han
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Min-Seok Choi
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, South Korea
| | - Jae-Sang Hong
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, South Korea
| | - Youngmo Seong
- Department of Bioscience and Biotechnology, Sejong University, Seoul, South Korea
| | - Young-Soo Kwon
- Department of Bioscience and Biotechnology, Sejong University, Seoul, South Korea
| | - Young Sik Lee
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, South Korea
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13
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Abstract
DROSHA is the catalytic subunit of the Microprocessor complex, which initiates microRNA (miRNA) maturation in the nucleus by recognizing and cleaving hairpin precursors embedded in primary transcripts. However, accumulating evidence suggests that not all hairpin substrates of DROSHA are associated with the generation of functional small RNAs. By targeting those hairpins, DROSHA regulates diverse aspects of RNA metabolism across the transcriptome, serves as a line of defense against the expression of potentially deleterious elements, and permits cell fate determination and differentiation. DROSHA is also versatile in the way that it executes these noncanonical functions, occasionally depending on its RNA-binding activity rather than its catalytic activity. Herein, we discuss the functional and mechanistic diversity of DROSHA beyond the miRNA biogenesis pathway in light of recent findings.
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Affiliation(s)
- Dooyoung Lee
- a Department of Agricultural Biotechnology , Seoul National University , Seoul , Republic of Korea
| | - Chanseok Shin
- a Department of Agricultural Biotechnology , Seoul National University , Seoul , Republic of Korea.,b Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute , Seoul National University , Seoul , Republic of Korea
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14
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Rodas-Junco BA, Canul-Chan M, Rojas-Herrera RA, De-la-Peña C, Nic-Can GI. Stem Cells from Dental Pulp: What Epigenetics Can Do with Your Tooth. Front Physiol 2017; 8:999. [PMID: 29270128 PMCID: PMC5724083 DOI: 10.3389/fphys.2017.00999] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/20/2017] [Indexed: 12/16/2022] Open
Abstract
Adult stem cells have attracted scientific attention because they are able to self-renew and differentiate into several specialized cell types. In this context, human dental tissue-derived mesenchymal stem cells (hDT-MSCs) have emerged as a possible solution for repairing or regenerating damaged tissues. These cells can be isolated from primary teeth that are naturally replaced, third molars, or other dental tissues and exhibit self-renewal, a high proliferative rate and a great multilineage potential. However, the cellular and molecular mechanisms that determine lineage specification are still largely unknown. It is known that a change in cell fate requires the deletion of existing transcriptional programs, followed by the establishment of a new developmental program to give rise to a new cell lineage. Increasing evidence indicates that chromatin structure conformation can influence cell fate. In this way, reversible chemical modifications at the DNA or histone level, and combinations thereof can activate or inactivate cell-type-specific gene sequences, giving rise to an alternative cell fates. On the other hand, miRNAs are starting to emerge as a possible player in establishing particular somatic lineages. In this review, we discuss two new and promising research fields in medicine and biology, epigenetics and stem cells, by summarizing the properties of hDT-MSCs and highlighting the recent findings on epigenetic contributions to the regulation of cellular differentiation.
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Affiliation(s)
- Beatriz A Rodas-Junco
- CONACYT-Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Michel Canul-Chan
- Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Rafael A Rojas-Herrera
- Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Geovanny I Nic-Can
- CONACYT-Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Mexico
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15
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Global analysis of AGO2-bound RNAs reveals that miRNAs induce cleavage of target RNAs with limited complementarity. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:1148-1158. [PMID: 29031931 DOI: 10.1016/j.bbagrm.2017.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/11/2017] [Accepted: 10/04/2017] [Indexed: 01/26/2023]
Abstract
Among the four Argonaute family members in mammals, only AGO2 protein retains endonuclease activity and facilitates cleavage of target RNAs base-pairing with highly complementary guide RNAs. Despite the deeply conserved catalytic activity, only a small number of targets have been reported to extensively base pair with cognate miRNAs to be cleaved by AGO2. Here, we analyzed AGO2-bound RNAs by CrossLinking ImmunoPrecipitation (CLIP) of genetically modified cells that express epitope-tagged AGO2 from the native genomic locus. We found that HMGA2 mRNA is cleaved by AGO2 loaded with let-7 and miR-21. In contrast to the generally accepted notion, the base-pairing from the seed region to the cleavage site, rather than perfect or near perfect complementarity, was required for cleavage of the target mRNA in cells. Non-templated addition of nucleotides at the 3' end of the cleaved RNA was observed, further supporting the AGO2-mediated cleavage. Based on the observation that the limited complementarity is the minimum requirement for cleavage, we found that AGO2-mediated cleavage of targets is more common than previously thought. Our result may explain the vital role of endonuclease activity in controlling miRNA-mediated gene regulation.
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16
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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17
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Marinaro F, Marzi MJ, Hoffmann N, Amin H, Pelizzoli R, Niola F, Nicassio F, De Pietri Tonelli D. MicroRNA-independent functions of DGCR8 are essential for neocortical development and TBR1 expression. EMBO Rep 2017; 18:603-618. [PMID: 28232627 DOI: 10.15252/embr.201642800] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 01/16/2017] [Accepted: 01/19/2017] [Indexed: 12/31/2022] Open
Abstract
Recent evidence indicates that the miRNA biogenesis factors DROSHA, DGCR8, and DICER exert non-overlapping functions, and have also roles in miRNA-independent regulatory mechanisms. However, it is currently unknown whether miRNA-independent functions of DGCR8 play any role in the maintenance of neuronal progenitors and during corticogenesis. Here, by phenotypic comparison of cortices from conditional Dgcr8 and Dicer knockout mice, we show that Dgcr8 deletion, in contrast to Dicer depletion, leads to premature differentiation of neural progenitor cells and overproduction of TBR1-positive neurons. Remarkably, depletion of miRNAs upon DCGR8 loss is reduced compared to DICER loss, indicating that these phenotypic differences are mediated by miRNA-independent functions of DGCR8. We show that Dgcr8 mutations induce an earlier and stronger phenotype in the developing nervous system compared to Dicer mutants and that miRNA-independent functions of DGCR8 are critical for corticogenesis. Finally, our data also suggest that the Microprocessor complex, with DROSHA and DGCR8 as core components, directly regulates the Tbr1 transcript, containing evolutionarily conserved hairpins that resemble miRNA precursors, independently of miRNAs.
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Affiliation(s)
- Federica Marinaro
- Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Matteo J Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan, Italy
| | - Nadin Hoffmann
- Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Hayder Amin
- Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Roberta Pelizzoli
- Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Francesco Niola
- Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan, Italy
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18
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Coffre M, Benhamou D, Rieß D, Blumenberg L, Snetkova V, Hines MJ, Chakraborty T, Bajwa S, Jensen K, Chong MMW, Getu L, Silverman GJ, Blelloch R, Littman DR, Calado D, Melamed D, Skok JA, Rajewsky K, Koralov SB. miRNAs Are Essential for the Regulation of the PI3K/AKT/FOXO Pathway and Receptor Editing during B Cell Maturation. Cell Rep 2016; 17:2271-2285. [PMID: 27880903 PMCID: PMC5679080 DOI: 10.1016/j.celrep.2016.11.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/14/2016] [Accepted: 10/26/2016] [Indexed: 12/20/2022] Open
Abstract
B cell development is a tightly regulated process dependent on sequential rearrangements of immunoglobulin loci that encode the antigen receptor. To elucidate the role of microRNAs (miRNAs) in the orchestration of B cell development, we ablated all miRNAs at the earliest stage of B cell development by conditionally targeting the enzymes critical for RNAi in early B cell precursors. Absence of any one of these enzymes led to a block at the pro- to pre-B cell transition due to increased apoptosis and a failure of pre-B cells to proliferate. Expression of a Bcl2 transgene allowed for partial rescue of B cell development, however, the majority of the rescued B cells had low surface immunoglobulin expression with evidence of ongoing light chain editing. Our analysis revealed that miRNAs are critical for the regulation of the PTEN-AKT-FOXO1 pathway that in turn controls Rag expression during B cell development.
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Affiliation(s)
- Maryaline Coffre
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - David Benhamou
- Department of Immunology, Faculty of Medicine, Technion, Haifa 31096, Israel
| | - David Rieß
- Harvard Medical School, Pathology, Boston, MA 02115, USA
| | - Lili Blumenberg
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Valentina Snetkova
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Marcus J Hines
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | | | - Sofia Bajwa
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Kari Jensen
- Harvard Medical School, Pathology, Boston, MA 02115, USA
| | - Mark M W Chong
- Skirball Institute, NYU School of Medicine, New York, NY 10016, USA
| | - Lelise Getu
- Department of Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Gregg J Silverman
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Department of Medicine, NYU School of Medicine, New York, NY 10016, USA
| | | | - Dan R Littman
- Skirball Institute, NYU School of Medicine, New York, NY 10016, USA; The HHMI, NYU School of Medicine, New York, NY 10016, USA
| | - Dinis Calado
- Harvard Medical School, Pathology, Boston, MA 02115, USA
| | - Doron Melamed
- Department of Immunology, Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Jane A Skok
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Klaus Rajewsky
- Harvard Medical School, Pathology, Boston, MA 02115, USA
| | - Sergei B Koralov
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
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19
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Rolando C, Erni A, Grison A, Beattie R, Engler A, Gokhale P, Milo M, Wegleiter T, Jessberger S, Taylor V. Multipotency of Adult Hippocampal NSCs In Vivo Is Restricted by Drosha/NFIB. Cell Stem Cell 2016; 19:653-662. [DOI: 10.1016/j.stem.2016.07.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 05/23/2016] [Accepted: 07/06/2016] [Indexed: 11/26/2022]
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20
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Dai L, Chen K, Youngren B, Kulina J, Yang A, Guo Z, Li J, Yu P, Gu S. Cytoplasmic Drosha activity generated by alternative splicing. Nucleic Acids Res 2016; 44:10454-10466. [PMID: 27471035 PMCID: PMC5137420 DOI: 10.1093/nar/gkw668] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 07/01/2016] [Accepted: 07/19/2016] [Indexed: 01/03/2023] Open
Abstract
RNase III enzyme Drosha interacts with DGCR8 to form the Microprocessor, initiating canonical microRNA (miRNA) maturation in the nucleus. Here, we re-evaluated where Drosha functions in cells using Drosha and/or DGCR8 knock out (KO) cells and cleavage reporters. Interestingly, a truncated Drosha mutant located exclusively in the cytoplasm cleaved pri-miRNA effectively in a DGCR8-dependent manner. In addition, we demonstrated that in vitro generated pri-miRNAs when transfected into cells could be processed to mature miRNAs in the cytoplasm. These results indicate the existence of cytoplasmic Drosha (c-Drosha) activity. Although a subset of endogenous pri-miRNAs become enriched in the cytoplasm of Drosha KO cells, it remains unclear whether pri-miRNA processing is the main function of c-Drosha. We identified two novel in-frame Drosha isoforms generated by alternative splicing in both HEK293T and HeLa cells. One isoform loses the putative nuclear localization signal, generating c-Drosha. Further analysis indicated that the c-Drosha isoform is abundant in multiple cell lines, dramatically variable among different human tissues and upregulated in multiple tumors, suggesting that c-Drosha plays a unique role in gene regulation. Our results reveal a new layer of regulation on the miRNA pathway and provide novel insights into the ever-evolving functions of Drosha.
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Affiliation(s)
- Lisheng Dai
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Kevin Chen
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Brenda Youngren
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Julia Kulina
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Acong Yang
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Zhengyu Guo
- Department of Electrical and Computer Engineering & TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Jin Li
- Department of Electrical and Computer Engineering & TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Peng Yu
- Department of Electrical and Computer Engineering & TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Shuo Gu
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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21
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Galka-Marciniak P, Olejniczak M, Starega-Roslan J, Szczesniak MW, Makalowska I, Krzyzosiak WJ. siRNA release from pri-miRNA scaffolds is controlled by the sequence and structure of RNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:639-49. [DOI: 10.1016/j.bbagrm.2016.02.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 01/17/2023]
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22
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Kwon YS, Song H. Analysis of microRNAs in a knock-in hESC line expressing epitope-tagged AGO2. Anim Cells Syst (Seoul) 2016. [DOI: 10.1080/19768354.2015.1137227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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23
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Belair CD, Paikari A, Moltzahn F, Shenoy A, Yau C, Dall'Era M, Simko J, Benz C, Blelloch R. DGCR8 is essential for tumor progression following PTEN loss in the prostate. EMBO Rep 2015. [PMID: 26206718 DOI: 10.15252/embr.201439925] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In human prostate cancer, the microRNA biogenesis machinery increases with prostate cancer progression. Here, we show that deletion of the Dgcr8 gene, a critical component of this complex, inhibits tumor progression in a Pten-knockout mouse model of prostate cancer. Early stages of tumor development were unaffected, but progression to advanced prostatic intraepithelial neoplasia was severely inhibited. Dgcr8 loss blocked Pten null-induced expansion of the basal-like, but not luminal, cellular compartment. Furthermore, while late-stage Pten knockout tumors exhibit decreased senescence-associated beta-galactosidase activity and increased proliferation, the simultaneous deletion of Dgcr8 blocked these changes resulting in levels similar to wild type. Sequencing of small RNAs in isolated epithelial cells uncovered numerous miRNA changes associated with PTEN loss. Consistent with a Pten-Dgcr8 association, analysis of a large cohort of human prostate tumors shows a strong correlation between Akt activation and increased Dgcr8 mRNA levels. Together, these findings uncover a critical role for microRNAs in enhancing proliferation and enabling the expansion of the basal cell compartment associated with tumor progression following Pten loss.
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Affiliation(s)
- Cassandra D Belair
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California - San Francisco, San Francisco, CA, USA Center for Reproductive Sciences, University of California - San Francisco, San Francisco, CA, USA Department of Urology, University of California - San Francisco, San Francisco, CA, USA
| | - Alireza Paikari
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California - San Francisco, San Francisco, CA, USA Center for Reproductive Sciences, University of California - San Francisco, San Francisco, CA, USA
| | - Felix Moltzahn
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California - San Francisco, San Francisco, CA, USA Department of Urology, University of California - San Francisco, San Francisco, CA, USA
| | - Archana Shenoy
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California - San Francisco, San Francisco, CA, USA Department of Urology, University of California - San Francisco, San Francisco, CA, USA
| | - Christina Yau
- Department of Medicine, University of California - San Francisco, San Francisco, CA, USA Buck Institute for Research on Aging, Novato, CA, USA
| | - Marc Dall'Era
- Department of Urology, University of California - San Francisco, San Francisco, CA, USA
| | - Jeff Simko
- Department of Urology, University of California - San Francisco, San Francisco, CA, USA Department of Anatomic Pathology, University of California - San Francisco, San Francisco, CA, USA
| | - Christopher Benz
- Department of Medicine, University of California - San Francisco, San Francisco, CA, USA Buck Institute for Research on Aging, Novato, CA, USA
| | - Robert Blelloch
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California - San Francisco, San Francisco, CA, USA Center for Reproductive Sciences, University of California - San Francisco, San Francisco, CA, USA Department of Urology, University of California - San Francisco, San Francisco, CA, USA Department of Anatomic Pathology, University of California - San Francisco, San Francisco, CA, USA
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24
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Parchem RJ, Moore N, Fish JL, Parchem JG, Braga TT, Shenoy A, Oldham MC, Rubenstein JLR, Schneider RA, Blelloch R. miR-302 Is Required for Timing of Neural Differentiation, Neural Tube Closure, and Embryonic Viability. Cell Rep 2015. [PMID: 26212322 PMCID: PMC4741278 DOI: 10.1016/j.celrep.2015.06.074] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The evolutionarily conserved miR-302 family of microRNAs is expressed during early mammalian embryonic development. Here, we report that deletion of miR-302a-d in mice results in a fully penetrant late embryonic lethal phenotype. Knockout embryos have an anterior neural tube closure defect associated with a thickened neuroepithelium. The neuroepithelium shows increased progenitor proliferation, decreased cell death, and precocious neuronal differentiation. mRNA profiling at multiple time points during neurulation uncovers a complex pattern of changing targets over time. Overexpression of one of these targets, Fgf15, in the neuroepithelium of the chick embryo induces precocious neuronal differentiation. Compound mutants between mir-302 and the related mir-290 locus have a synthetic lethal phenotype prior to neurulation. Our results show that mir-302 helps regulate neurulation by suppressing neural progenitor expansion and precocious differentiation. Furthermore, these results uncover redundant roles for mir-290 and mir-302 early in development.
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Affiliation(s)
- Ronald J Parchem
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nicole Moore
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jennifer L Fish
- Department of Orthopaedic Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jacqueline G Parchem
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tarcio T Braga
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Archana Shenoy
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael C Oldham
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John L R Rubenstein
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Richard A Schneider
- Department of Orthopaedic Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robert Blelloch
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA.
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25
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Shenoy A, Danial M, Blelloch RH. Let-7 and miR-125 cooperate to prime progenitors for astrogliogenesis. EMBO J 2015; 34:1180-94. [PMID: 25715649 DOI: 10.15252/embj.201489504] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 01/16/2015] [Indexed: 01/09/2023] Open
Abstract
The molecular basis of astrocyte differentiation and maturation is poorly understood. As microRNAs have important roles in cell fate transitions, we set out to study their function during the glial progenitor cell (GPC) to astrocyte transition. Inducible deletion of all canonical microRNAs in GPCs in vitro led to a block in the differentiation to astrocytes. In an unbiased screen, the reintroduction of let-7 and miR-125 families of microRNAs rescued differentiation. Let-7 and miR-125 shared many targets and functioned in parallel to JAK-STAT signaling, a known regulator of astrogliogenesis. While individual knockdown of shared targets did not rescue the differentiation phenotype in microRNA-deficient GPCs, overexpression of these targets in wild-type GPCs blocked differentiation. This finding supports the idea that microRNAs simultaneously suppress multiple mRNAs that inhibit differentiation. MicroRNA-regulated transcripts exhibited concordant changes during in vivo differentiation and were enriched for a gene set upregulated in glioblastomas, consistent with validity of using the in vitro model to study in vivo events. These findings provide insight into the microRNAs and the genes they regulate in this important cell fate transition.
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Affiliation(s)
- Archana Shenoy
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Muhammad Danial
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Robert H Blelloch
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Department of Urology, University of California San Francisco, San Francisco, CA, USA
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